Quartz diorite bedrock underlying the Luquillo Mountains of eastern Puerto Rico undergoes weathering at one of the fastest documented rates for granitic rocks in the world. Although tropical temperatures and precipitation promote rapid weathering in this location, increased bacterial densities in the regolith immediately above the bedrock suggest that microorganisms contribute to mineral weathering as well. Deep saprolite and saprock samples were obtained at the bedrock interface in an upland location (Guaba Ridge) in the Rio Icacos watershed for examination by environmental scanning electron microscopy (ESEM). In ESEM images, mineral nanotubes were observed to occur frequently in association with coccus- and rod-shaped structures resembling bacteria. These nanotubes (50–140-nm width and 150–2700-nm length) were identified as halloysite using transmission electron microscopy. Observations of multiple nanotubes on the surfaces of an individual cell are consistent with the cell's exterior functional groups interacting with Si in pore water to facilitate halloysite nucleation. We propose that one mechanism by which bacteria contribute to the rapid weathering of quartz diorite minerals in this regolith is by lowering the free energy for secondary mineral formation. The presence of bacterial surfaces may result in more rapid removal of Si from solution, thereby increasing the dissolution rates of primary minerals.